RepairFastq
Join single end reads to paired end
Usage
Usage: java -jar dist/repairfastq.jar [options] Files
Usage: repairfastq [options] Files
Options:
--R2
fastq output for R2 reads.
--Rx
fastq output for other reads.
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--maxRecordsInRam
When writing files that need to be sorted, this will specify the number
of records stored in RAM before spilling to disk. Increasing this number
reduces the number of file handles needed to sort a file, and increases
the amount of RAM needed
Default: 50000
--md5
create MD5 checksum.
Default: false
-o, --output, --R1
output for R1 reads. Output file. Optional . Default: stdout
--tmpDir
tmp working directory. Default: java.io.tmpDir
Default: []
--version
print version and exit
Keywords
- fastq
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew repairfastq
The java jar file will be installed in the dist
directory.
Creation Date
20240128
Source code
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite repairfastq ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030